diff --git a/src/renderer/src/components/WorktreeJumpPalette.tsx b/src/renderer/src/components/WorktreeJumpPalette.tsx
index c034994f1..de0259c15 100644
--- a/src/renderer/src/components/WorktreeJumpPalette.tsx
+++ b/src/renderer/src/components/WorktreeJumpPalette.tsx
@@ -40,6 +40,7 @@ import StatusIndicator from '@/components/sidebar/StatusIndicator'
 import { cn } from '@/lib/utils'
 import { getWorktreeStatus, getWorktreeStatusLabel } from '@/lib/worktree-status'
 import { activateAndRevealWorktree } from '@/lib/worktree-activation'
+import { queueWorkspaceActivationTerminalFocus } from '@/lib/workspace-activation-terminal-focus'
 import { findWorktreeById } from '@/store/slices/worktree-helpers'
 import {
   getWorktreePaletteSearchScope,
@@ -1271,12 +1272,16 @@ export default function WorktreeJumpPalette(): React.JSX.Element | null {
         )
         return
       }
-      activateAndRevealWorktree(worktreeId)
+      const activation = activateAndRevealWorktree(worktreeId)
       recordFeatureInteraction('cmd-j-workspace-open')
       skipRestoreFocusRef.current = true
       closeModal()
       setSelectedItemId('')
-      focusFallbackSurface()
+      // Why: #9939 — the unscoped fallback grabs the first terminal in the document, which is
+      // often the worktree we just left, now hidden. Focus the destination's own tab instead.
+      if (!queueWorkspaceActivationTerminalFocus(worktreeId, activation)) {
+        focusFallbackSurface()
+      }
     },
     [closeModal, focusFallbackSurface, recordFeatureInteraction]
   )
@@ -1445,7 +1450,9 @@ export default function WorktreeJumpPalette(): React.JSX.Element | null {
         return
       }
       if (previousWorktreeIdRef.current) {
-        focusFallbackSurface()
+        // Why: #9939 — sidebar reveal keeps the same worktree, so restore the exact element the
+        // user came from rather than the first terminal in the document.
+        focusFallbackSurface(previousFocusElementRef.current)
       }
     },
     [
@@ -1516,7 +1523,9 @@ export default function WorktreeJumpPalette(): React.JSX.Element | null {
       const activeMatch = matches.find((w) => w.repoId === state.activeRepoId) ?? matches[0]
       if (activeMatch) {
         closeModal()
-        activateAndRevealWorktree(activeMatch.id)
+        // Why: #9939 — jumping to an already-open workspace must focus its own terminal.
+        const activation = activateAndRevealWorktree(activeMatch.id)
+        queueWorkspaceActivationTerminalFocus(activeMatch.id, activation)
         recordFeatureInteraction('cmd-j-workspace-open')
         return
       }
@@ -1543,7 +1552,9 @@ export default function WorktreeJumpPalette(): React.JSX.Element | null {
       const activeMatch = matches.find((w) => w.repoId === state.activeRepoId) ?? matches[0]
       if (activeMatch) {
         closeModal()
-        activateAndRevealWorktree(activeMatch.id)
+        // Why: #9939 — jumping to an already-open workspace must focus its own terminal.
+        const activation = activateAndRevealWorktree(activeMatch.id)
+        queueWorkspaceActivationTerminalFocus(activeMatch.id, activation)
         recordFeatureInteraction('cmd-j-workspace-open')
         return
       }
diff --git a/src/renderer/src/components/cmd-j/palette-activation-focus-routing.test.ts b/src/renderer/src/components/cmd-j/palette-activation-focus-routing.test.ts
new file mode 100644
index 000000000..0222a0191
--- /dev/null
+++ b/src/renderer/src/components/cmd-j/palette-activation-focus-routing.test.ts
@@ -0,0 +1,58 @@
+import { readFileSync } from 'node:fs'
+import { join } from 'node:path'
+import { describe, expect, it } from 'vitest'
+
+// Why: happy-dom does not reproduce Chromium's display:none focus no-op, so the #9939 regression
+// is invisible to behavioral tests. Pin the routing decision at the source level instead.
+function paletteSource(): string {
+  return readFileSync(join(__dirname, '..', 'WorktreeJumpPalette.tsx'), 'utf8')
+}
+
+function sourceBetween(source: string, startPattern: string, endPattern: string): string {
+  const start = source.indexOf(startPattern)
+  expect(start).toBeGreaterThanOrEqual(0)
+  const end = source.indexOf(endPattern, start + startPattern.length)
+  expect(end).toBeGreaterThan(start)
+  return source.slice(start, end)
+}
+
+describe('Cmd+J activation focus routing (#9939)', () => {
+  it('routes worktree selection through the scoped helper before any unscoped fallback', () => {
+    const handler = sourceBetween(
+      paletteSource(),
+      'const handleSelectWorktree = useCallback',
+      'const handleSelectBrowserPage'
+    )
+
+    expect(handler).toContain('queueWorkspaceActivationTerminalFocus(worktreeId, activation)')
+    // The fallback must be reachable only when the helper declines the destination.
+    expect(handler).toMatch(
+      /if \(!queueWorkspaceActivationTerminalFocus\(worktreeId, activation\)\) \{\s*focusFallbackSurface\(\)\s*\}/
+    )
+    // An unconditional fallback is the exact shape of the original bug, so the only bare call
+    // allowed is the guarded one inside the if-block above.
+    expect(handler.match(/focusFallbackSurface\(\)/g)?.length).toBe(1)
+  })
+
+  it('restores the pre-palette element for project targets instead of the first terminal found', () => {
+    const handler = sourceBetween(
+      paletteSource(),
+      'const handleSelectProjectTarget = useCallback',
+      'const handleSelectItem = useCallback'
+    )
+
+    expect(handler).toContain('focusFallbackSurface(previousFocusElementRef.current)')
+    expect(handler).not.toMatch(/focusFallbackSurface\(\)/)
+  })
+
+  it('focuses the destination workspace when jumping to an already-open issue match', () => {
+    const source = paletteSource()
+    const activationCalls =
+      source.match(/const activation = activateAndRevealWorktree\(activeMatch\.id\)/g)?.length ?? 0
+    // Both issue-number match paths (PR and issue lookup) must focus the destination.
+    expect(activationCalls).toBe(2)
+    expect(
+      source.match(/queueWorkspaceActivationTerminalFocus\(activeMatch\.id, activation\)/g)?.length
+    ).toBe(activationCalls)
+  })
+})
diff --git a/src/renderer/src/hooks/useComposerState.ts b/src/renderer/src/hooks/useComposerState.ts
index 1d9a4d9d5..2411ed3b9 100644
--- a/src/renderer/src/hooks/useComposerState.ts
+++ b/src/renderer/src/hooks/useComposerState.ts
@@ -145,7 +145,7 @@ import {
   type ExecutionHostId
 } from '../../../shared/execution-host'
 import { getHostDisplayLabelOverrides } from '../../../shared/host-setting-overrides'
-import { queueNewWorkspaceTerminalFocus } from '@/lib/new-workspace-terminal-focus'
+import { queueWorkspaceActivationTerminalFocus } from '@/lib/workspace-activation-terminal-focus'
 import { getSettingsForRepoRuntimeOwner } from '@/lib/repo-runtime-owner'
 import { getSuggestedCreatureName } from '@/components/sidebar/worktree-name-suggestions'
 import type { SmartWorkspaceNameSelection } from '@/components/new-workspace/SmartWorkspaceNameField'
@@ -3560,7 +3560,7 @@ export function useComposerState(options: UseComposerStateOptions): UseComposerS
         clearNewWorkspaceDraft()
       }
       onCreated?.()
-      queueNewWorkspaceTerminalFocus(worktree.id, activation)
+      queueWorkspaceActivationTerminalFocus(worktree.id, activation)
     } catch (error) {
       const formattedError = formatWorkspaceCreateError(error)
       setCreateError(formattedError)
diff --git a/src/renderer/src/lib/new-workspace-terminal-focus.test.ts b/src/renderer/src/lib/workspace-activation-terminal-focus.test.ts
similarity index 63%
rename from src/renderer/src/lib/new-workspace-terminal-focus.test.ts
rename to src/renderer/src/lib/workspace-activation-terminal-focus.test.ts
index 62decac8b..74e95953c 100644
--- a/src/renderer/src/lib/new-workspace-terminal-focus.test.ts
+++ b/src/renderer/src/lib/workspace-activation-terminal-focus.test.ts
@@ -18,7 +18,7 @@ vi.mock('@/store', () => ({
   }
 }))
 
-import { queueNewWorkspaceTerminalFocus } from './new-workspace-terminal-focus'
+import { queueWorkspaceActivationTerminalFocus } from './workspace-activation-terminal-focus'
 
 type FocusState = {
   activeWorktreeId: string | null
@@ -39,7 +39,7 @@ function flushFrame(): void {
   frame?.()
 }
 
-describe('queueNewWorkspaceTerminalFocus', () => {
+describe('queueWorkspaceActivationTerminalFocus', () => {
   beforeEach(() => {
     vi.clearAllMocks()
     pendingFrame = null
@@ -58,7 +58,7 @@ describe('queueNewWorkspaceTerminalFocus', () => {
       activeTabId: 'tab-1'
     })
 
-    queueNewWorkspaceTerminalFocus('wt-1', { primaryTabId: 'tab-1' })
+    queueWorkspaceActivationTerminalFocus('wt-1', { primaryTabId: 'tab-1' })
 
     expect(focusRuntimeTerminalSurfaceMock).not.toHaveBeenCalled()
     flushFrame()
@@ -75,7 +75,7 @@ describe('queueNewWorkspaceTerminalFocus', () => {
       activeTabId: 'tab-adopted'
     })
 
-    queueNewWorkspaceTerminalFocus('wt-1', { primaryTabId: null })
+    queueWorkspaceActivationTerminalFocus('wt-1', { primaryTabId: null })
     flushFrame()
 
     expect(focusRuntimeTerminalSurfaceMock).toHaveBeenCalledWith('tab-adopted')
@@ -91,13 +91,51 @@ describe('queueNewWorkspaceTerminalFocus', () => {
       activeTabId: 'tab-1'
     })
 
-    queueNewWorkspaceTerminalFocus('wt-1', { primaryTabId: 'tab-1' })
+    queueWorkspaceActivationTerminalFocus('wt-1', { primaryTabId: 'tab-1' })
     flushFrame()
 
     expect(focusRuntimeTerminalSurfaceMock).toHaveBeenCalledWith('tab-1')
     expect(focusTerminalTabSurfaceMock).not.toHaveBeenCalled()
   })
 
+  // Why: #9939 — the return value is what stops the palette from running its whole-document
+  // fallback, which would grab the worktree the user just left, now mounted but hidden.
+  it('reports that it claimed focus for a terminal destination', () => {
+    setFocusState({
+      activeWorktreeId: 'wt-1',
+      activeView: 'terminal',
+      activeTabType: 'terminal',
+      activeTabId: 'tab-adopted'
+    })
+
+    expect(queueWorkspaceActivationTerminalFocus('wt-1', { primaryTabId: null })).toBe(true)
+  })
+
+  it('declines a destination whose restored surface is not a terminal', () => {
+    setFocusState({
+      activeWorktreeId: 'wt-1',
+      activeView: 'terminal',
+      activeTabType: 'browser',
+      activeTabId: 'tab-adopted'
+    })
+
+    expect(queueWorkspaceActivationTerminalFocus('wt-1', { primaryTabId: null })).toBe(false)
+    flushFrame()
+    expect(focusRuntimeTerminalSurfaceMock).not.toHaveBeenCalled()
+    expect(focusTerminalTabSurfaceMock).not.toHaveBeenCalled()
+  })
+
+  it('declines a destination that has no terminal tab yet', () => {
+    setFocusState({
+      activeWorktreeId: 'wt-1',
+      activeView: 'terminal',
+      activeTabType: 'terminal',
+      activeTabId: null
+    })
+
+    expect(queueWorkspaceActivationTerminalFocus('wt-1', { primaryTabId: null })).toBe(false)
+  })
+
   it('does not steal focus if the user leaves the created workspace first', () => {
     const state: FocusState = {
       activeWorktreeId: 'wt-1',
@@ -107,7 +145,7 @@ describe('queueNewWorkspaceTerminalFocus', () => {
     }
     setFocusState(state)
 
-    queueNewWorkspaceTerminalFocus('wt-1', { primaryTabId: 'tab-1' })
+    queueWorkspaceActivationTerminalFocus('wt-1', { primaryTabId: 'tab-1' })
     state.activeWorktreeId = 'wt-2'
     flushFrame()
 
diff --git a/src/renderer/src/lib/new-workspace-terminal-focus.ts b/src/renderer/src/lib/workspace-activation-terminal-focus.ts
similarity index 76%
rename from src/renderer/src/lib/new-workspace-terminal-focus.ts
rename to src/renderer/src/lib/workspace-activation-terminal-focus.ts
index 8a5aa6ce3..7ef6f61ec 100644
--- a/src/renderer/src/lib/new-workspace-terminal-focus.ts
+++ b/src/renderer/src/lib/workspace-activation-terminal-focus.ts
@@ -3,7 +3,7 @@ import { focusTerminalTabSurface } from '@/lib/focus-terminal-tab-surface'
 import { focusRuntimeTerminalSurface } from '@/runtime/sync-runtime-graph'
 import type { ActivateAndRevealResult } from '@/lib/worktree-activation'
 
-function resolveCreatedWorkspaceTerminalTabId(
+function resolveActivatedWorkspaceTerminalTabId(
   worktreeId: string,
   activation: ActivateAndRevealResult | false
 ): string | null {
@@ -21,13 +21,15 @@ function resolveCreatedWorkspaceTerminalTabId(
   return state.activeTabId
 }
 
-export function queueNewWorkspaceTerminalFocus(
+// Why: returns false when the destination's restored surface is not a terminal, so callers can
+// fall back instead of focusing an unrelated worktree's mounted-but-hidden terminal (#9939).
+export function queueWorkspaceActivationTerminalFocus(
   worktreeId: string,
   activation: ActivateAndRevealResult | false
-): void {
-  const tabId = resolveCreatedWorkspaceTerminalTabId(worktreeId, activation)
+): boolean {
+  const tabId = resolveActivatedWorkspaceTerminalTabId(worktreeId, activation)
   if (!tabId) {
-    return
+    return false
   }
 
   requestAnimationFrame(() => {
@@ -48,4 +50,5 @@ export function queueNewWorkspaceTerminalFocus(
       focusTerminalTabSurface(tabId)
     }
   })
+  return true
 }
diff --git a/src/renderer/src/lib/worktree-creation-flow.test.ts b/src/renderer/src/lib/worktree-creation-flow.test.ts
index f614c679c..90af3fe69 100644
--- a/src/renderer/src/lib/worktree-creation-flow.test.ts
+++ b/src/renderer/src/lib/worktree-creation-flow.test.ts
@@ -57,8 +57,8 @@ vi.mock('@/lib/worktree-activation', () => ({
   ensureWorktreeHasInitialTerminal: vi.fn()
 }))
 
-vi.mock('@/lib/new-workspace-terminal-focus', () => ({
-  queueNewWorkspaceTerminalFocus: vi.fn()
+vi.mock('@/lib/workspace-activation-terminal-focus', () => ({
+  queueWorkspaceActivationTerminalFocus: vi.fn()
 }))
 
 vi.mock('@/lib/new-workspace', () => ({
@@ -80,7 +80,7 @@ import {
   activateAndRevealWorktree,
   ensureWorktreeHasInitialTerminal
 } from '@/lib/worktree-activation'
-import { queueNewWorkspaceTerminalFocus } from '@/lib/new-workspace-terminal-focus'
+import { queueWorkspaceActivationTerminalFocus } from '@/lib/workspace-activation-terminal-focus'
 import {
   beginBackgroundWorktreePreparation,
   continueBackgroundWorktreeCreation,
@@ -498,7 +498,7 @@ describe('staged background worktree creation', () => {
       undefined,
       { activateCreatedTabs: false }
     )
-    expect(queueNewWorkspaceTerminalFocus).not.toHaveBeenCalled()
+    expect(queueWorkspaceActivationTerminalFocus).not.toHaveBeenCalled()
     expect(store.removePendingWorktreeCreation).toHaveBeenCalledWith('creation-1', {
       cleanupVm: false
     })
diff --git a/src/renderer/src/lib/worktree-creation-flow.ts b/src/renderer/src/lib/worktree-creation-flow.ts
index a975405de..dcfc25a33 100644
--- a/src/renderer/src/lib/worktree-creation-flow.ts
+++ b/src/renderer/src/lib/worktree-creation-flow.ts
@@ -8,7 +8,7 @@ import {
   type WorktreeStartupPayload
 } from '@/lib/worktree-activation'
 import { ensureAgentStartupInTerminal } from '@/lib/new-workspace'
-import { queueNewWorkspaceTerminalFocus } from '@/lib/new-workspace-terminal-focus'
+import { queueWorkspaceActivationTerminalFocus } from '@/lib/workspace-activation-terminal-focus'
 import { getActiveRuntimeTarget } from '@/runtime/runtime-rpc-client'
 import {
   attachEphemeralVmRuntimeToWorkspace,
@@ -273,7 +273,7 @@ async function executeWorktreeCreation(
     })
   }
   if (shouldActivateOnCompletion && !preparedRequest.suppressTerminalFocusOnCompletion) {
-    queueNewWorkspaceTerminalFocus(worktree.id, activation)
+    queueWorkspaceActivationTerminalFocus(worktree.id, activation)
   }
 
   // Why: awaiting the note IPC before the swap would add a visible round-trip to